I have downloaded R version 2.1.1 via apt-get and have now a running R under Ubuntu Breezy Badger. But now I would like to use the Bioconductor packages and tried to install with BioC(). No matter if I use the root account or my personal login, I always end up with at least 11 to 14 warnings and always the problem that all packages dependent on the Biobase package can not be installed. I should mention that I gave myself permission to all libraries and anyhow, other libraries such as limma are not affected. Warning messages: 1: installation of package 'Biobase' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 2: installation of package 'Biostrings' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 3: installation of package 'pamr' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 4: installation of package 'affy' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 5: installation of package 'annaffy' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 6: installation of package 'edd' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 7: installation of package 'genefilter' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 8: installation of package 'multtest' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 9: installation of package 'vsn' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 10: installation of package 'geneplotter' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 11: installation of package 'makecdfenv' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 12: installation of package 'matchprobes' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 13: installation of package 'gcrma' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 14: installation of package 'affyPLM' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... So when I try to open affy the following error message appears. > library(affy) Loading required package: Biobase Error in library.dynam(lib, package, package.lib) : shared library 'Biobase' not found In addition: Warning messages: 1: package 'Biobase' contains no R code in: loadNamespace(package, c(which.lib.loc, lib.loc)) 2: S3 method ?as.data.frame.exprSet? was declared in NAMESPACE but not found Error: package 'Biobase' could not be loaded I used the woody URL to apt-get install, but I guess that should not make a difference. I checked the mail archive, but somehow this particular problem was not discussed. It seems that something goes wrong during compiling the Biobase package. Any suggestions would be very welcome, I am not necessarily an expert on Linux. Greetings and thanks in advance, Anja Schiel

Hi Anja, If you are using R 2.1.1, could you upgrade to R 2.2.0, which is the latest versionof R, please? After you upgrade to R 2.2.0, you can use the biocLite script to install BioConductor for you. In an R command window, type the following: source("http://www.bioconductor.org/biocLite.R") biocLite() Please refer to the "Install - How To" page on the BioConductor official website. If you still have trouble in installing BioConductor, please report the error/warning messages and the result of sessionInfo() to the list again. HTH, Ting-Yuan ______________________________________ Ting-Yuan Liu Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center Seattle, WA, USA ______________________________________ On Sat, 26 Nov 2005, Anja Schiel wrote: > I have downloaded R version 2.1.1 via apt-get and have now a running R under Ubuntu Breezy Badger. But now I would like to use the Bioconductor packages and tried to install with BioC(). No matter if I use the root account or my personal login, I always end up with at least 11 to 14 warnings and always the problem that all packages dependent on the Biobase package can not be installed. I should mention that I gave myself permission to all libraries and anyhow, other libraries such as limma are not affected. Warning messages: 1: installation of package 'Biobase' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 2: installation of package 'Biostrings' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 3: installation of package 'pamr' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 4: installation of package 'affy' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 5: installation of package 'annaffy' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 6: installation of package 'edd' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 7: installation of package 'genefilter' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 8: installation of package 'multtest' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 9: installation of package 'vsn' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 10: installation of package 'geneplotter' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 11: installation of package 'makecdfenv' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 12: installation of package 'matchprobes' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 13: installation of package 'gcrma' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... 14: installation of package 'affyPLM' had non-zero exit status in: install.packages(pkgs = c("affy", "affydata", "affyPLM", "annaffy", ... So when I try to open affy the following error message appears. > library(affy) Loading required package: Biobase Error in library.dynam(lib, package, package.lib) : shared library 'Biobase' not found In addition: Warning messages: 1: package 'Biobase' contains no R code in: loadNamespace(package, c(which.lib.loc, lib.loc)) 2: S3 method ?as.data.frame.exprSet? was declared in NAMESPACE but not found Error: package 'Biobase' could not be loaded I used the woody URL to apt-get install, but I guess that should not make a difference. I checked the mail archive, but somehow this particular problem was not discussed. It seems that something goes wrong during compiling the Biobase package. Any suggestions would be very welcome, I am not necessarily an expert on Linux. Greetings and thanks in advance, Anja Schiel _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor